Email Templates Missing Links

I’ve been using a standard set of branded email templates based on an Infusionsoft template for a while now and just noticed that the links seem not to have transferred to my saved templates. I have a header with links to our home page and a few other pages on our site and a footer with a link to manage preferences. Has anyone else had this problem? Do you have to re-set every standardized link every time you use a template? It seems crazy that the URLs wouldn’t be saved to the template!